Global minimum energy structure

A related study was the exhaustive enumeration of the global minimum energy structure for all iP possible sequences of the HP model described in Section 10.3.1 [Li et al. 1996 Ihis showed that 4 75% of these sequences have a unique ground state (i.e. just on... 

Figure 5.6 A representation of the change in the value of is-rotai demonstrating how the computation could stop at a local (X) rather than the true (global) minimum value. The use of molecular dynamics gives the structure kinetic energy which allows it to overcome energy barriers, such as Y, to reach the global minimum energy structure of the molecule...

Figure 23 Stereo view of the global minimum-energy structure of Met-enkephalin in the absence of water.177...

Figure 36 Progress of the MCM procedure, starting from two different initial randomly chosen conformations of Met-enkephalin (a and b). In each of the two cases, the ECEPP energy and the root-mean-square deviation with respect to the global minimum-energy structure are shown.222...

Figure 12.2. Global minimum energy structures determined by full optimization at the B3LYP/6-31G level of a trifluoromethanesulfonic acid molecule with different numbers of water molecules, showing the 0-0 and O-H (in brackets) distances, and revealing that with (a) 1 and (b) 2 water molecules, the proton does not dissociate with (c) 3, (d) 4, and (e) 5 water molecules, the proton is dissociated forming a contact hydronium ion-sulfonate pair. Redrawn from results first presented in Ref. [23].

Somewhat later, Marshall and co-workers showed that the bioactive conformation need not be the global minimum energy structure. Furthermore, they emphasized that in the small molecule-macromolecule complex, the macromolecule occupies certain regions in space near the small molecule (otherwise there would be no complex formed), and that thus one would expect to find certain molecules to be inactive because when juxtaposed they collide with the macromolecule. Most modeling studies of the bioaaivity of small molecules... 

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